[gmx-users] Gromacs on Gigabit Ethernet Dual Opteron Cluster

[Ghermes Chilov]

Hi!

D> On Wed, 2003-10-01 at 18:53, Ghermes Chilov wrote:

>> I've got preliminary results of Gromacs's performance on Dual Opteron
>> cluster (Gigabit Ethernet, LAM-MPI 7.0). The scalability is good (>80%)
>> with up to 3 nodes used, but than it drops (44% for 8 nodes) and this
>> decrease seems to correlate with CPU load (which also drops from
>> 100-95% for 1 node to 60% for 8 nodes).
>> 
>> Should I play with LAM compilation options or go fishing somewhere
>> else? Probably parameters --with-tcp-short and --with-shm-short for
>> Gigabit Ethernet may be increased? (with respect to 500 kb for Fast
>> Ethernet).
D> which system do you use?

D> I'd suggest starting with the DPPC benchmark. Don't forget to use
D> -shuffle for grompp

AF> What system are you benchmarking with? It should be big enough,
AF> like the 'dppc' from the benchmarks suite.

The system (dummified protein in water)is big enough:~ 107.000 atoms,
-shuffle -sort were used.

I hope new scaling benchmarks on Myrinet will be available soon
(also for DPPC).

Ghermes